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Circomics of Cuban geminiviruses reveals the first alpha-satellite DNA in the Caribbean

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Abstract

Circomics (circular DNA genomics), the combination of rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) analysis and pyro-sequencing, has been used recently to identify geminiviruses with high efficiency and low costs. Circular DNAs associated with Cuban geminiviruses were characterised by RCA/RFLP analysis and 454 sequencing of two batches of DNA amplified from selected plant samples as well as individual cloning and Sanger sequencing of DNA components and compared to other geminiviral DNAs by phylogenetic analysis. Cuban geminiviruses that were closely related to each other challenged the circomics approach. Ten geminiviral components and one alpha-satellite DNA were determined and compared to three geminiviral components obtained by conventional cloning. New strains of Sida yellow mottle virus (SiYMoV), tomato yellow distortion leaf virus (ToYDLV), Sida golden mosaic Florida virus (SiGMFV) and Sida golden mosaic Liguanea virus (SiGMLV) are described with host plant species being classified by molecular PCR-based bar coding. A new virus species is named Peristrophe mosaic virus. The first alpha-satellite found in Middle America establishes the New World branch of these elements which are related to nanoviruses and were previously thought to be restricted to the Old World. In conclusion, circomics is efficient for complex infections and closely related viruses to detected unexpected viral DNAs, but may need some scrutinisation by direct sequencing and cloning of individual components for certain cases.

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Notes

  1. The terminology of America's subdivisions is quite complex and influenced by political and cultural conditions. Here, we refer only to the geographical term Middle America which includes the region south of the USA and north of Colombia/Venezuela in our description (see http://en.wikipedia.org/wiki/Americas_(terminology) for alternatives).

References

  1. H. Jeske, in Torque Teno Virus: The Still Elusive Human Pathogens, ed. by H. Zur Hausen, E.-M. de Villiers (Springer, Berlin, 2009), pp. 185–226

    Google Scholar 

  2. P.S. Wyant, S. Strohmeier, B. Schäfer, B. Krenz, I.P. Assunção, G.A. de Andrade Lima, H. Jeske, Virology 427, 151–157 (2012)

    Article  PubMed  CAS  Google Scholar 

  3. C. Hagen, A. Frizzi, S. Gabriels, M. Huang, R. Salati, B. Gabor, H. Huang, Arch. Virol. 157, 907–915 (2012)

    Article  PubMed  CAS  Google Scholar 

  4. R.W. Briddon, J. Stanley, Virology 344, 198–210 (2006)

    Article  PubMed  CAS  Google Scholar 

  5. T. Paprotka, V. Metzler, H. Jeske, Virology 404, 148–157 (2010)

    Article  PubMed  CAS  Google Scholar 

  6. G. Romay, D. Chirinos, F. Geraud-Pouey, C. Desbiez, Arch. Virol. 155, 1843–1847 (2010)

    Article  PubMed  CAS  Google Scholar 

  7. B. Gronenborn, Vet. Microbiol. 98, 103–109 (2004)

    Article  PubMed  CAS  Google Scholar 

  8. H. Jeske, M. Lütgemeier, W. Preiss, EMBO J. 20, 6158–6167 (2001)

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  9. W.J. Kress, K.J. Wurdack, E.A. Zimmer, L.A. Weig, D.H. Janzen, Proc. Natl. Acad. Sci. USA 102, 8369–8374 (2005)

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  10. T.A. Hall, Nucl. Acids Symp. Ser. 41, 95–98. http://www.mbio.ncsu.edu/BioEdit/BioEdit.html (1999)

  11. T. Hall, GERF Bull. Biosci. 2, 60–61 (2011)

    Google Scholar 

  12. M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson, D.G. Higgins, Bioinformatics 23, 2947–2948 (2007)

    Article  PubMed  CAS  Google Scholar 

  13. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, S. Kumar, Mol. Biol. Evol. 28, 2731–2739 (2011)

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  14. T. Paprotka, L.S. Boiteux, M.E.N. Fonseca, R.O. Resende, H. Jeske, J.C. Faria, S.G. Ribeiro, Virus Res. 149, 224–233 (2010)

    Article  PubMed  CAS  Google Scholar 

  15. H. Jeske, D. Gotthardt, S. Kober, J. Virol. Methods 163, 301–308 (2010)

    Article  PubMed  CAS  Google Scholar 

  16. C. Wege, R.D. Gotthardt, T. Frischmuth, H. Jeske, Arch. Virol. 145, 2217–2225 (2000)

    Article  PubMed  CAS  Google Scholar 

  17. J. Schubert, A. Habekuß, K. Kazmaier, H. Jeske, Virus Res. 127, 61–70 (2007)

    Article  PubMed  CAS  Google Scholar 

  18. P.S. Wyant, S. Kober, A. Schwierzok, C. Kocher, B. Schäfer, H. Jeske, C. Wege, Virus Res. 167, 397–403 (2012)

    Article  PubMed  CAS  Google Scholar 

  19. E. Fiallo-Olive, Y. Martinez-Zubiaur, E. Moriones, J. Navas-Castillo, Arch. Virol. 155, 1535–1537 (2010)

    Article  PubMed  CAS  Google Scholar 

  20. E. Fiallo-Olive, J. Navas-Castillo, E. Moriones, Y. Martinez-Zubiaur, Arch. Virol. 155, 2053–2058 (2010)

    Article  PubMed  CAS  Google Scholar 

  21. Y. Martinez, C. deBlas, I. Zabalgogeazcoa, M. Quinones, C. Castellanos, E.F. Peralta, J. Romero, Plant Dis. 81, 1215 (1997)

    Article  Google Scholar 

  22. Y.M. Zubiaur, C. de Blas, M. Quinones, C. Castellanos, E.L. Peralta, J. Romero, Arch. Virol. 143, 1757–1772 (1998)

    Article  CAS  Google Scholar 

  23. C.M. Fauquet, R.W. Briddon, J.K. Brown, E. Moriones, J. Stanley, M. Zerbini, X. Zhou, Arch. Virol. 153, 783–821 (2008)

    Article  PubMed  CAS  Google Scholar 

  24. P. Lotrakul, R.A. Valverde, A.D. Landry, Phytopathology 90, 723–729 (2000)

    Article  PubMed  CAS  Google Scholar 

  25. C. Ha, S. Coombs, P. Revill, R. Harding, M. Vu, J. Dale, J. Gen. Virol. 89, 312–326 (2008)

    Article  PubMed  CAS  Google Scholar 

  26. C. Ha, S. Coombs, P. Revill, R. Harding, M. Vu, J. Dale, J. Gen. Virol. 87, 997–1003 (2006)

    Article  PubMed  CAS  Google Scholar 

  27. A.M. Idris, M.S. Shahid, R.W. Briddon, A.J. Khan, J.K. Zhu, J.K. Brown, J. Gen. Virol. 92, 706–717 (2011)

    Article  PubMed  CAS  Google Scholar 

  28. V. Zaffalon, S.K. Mukherjee, V.S. Reddy, J.R. Thompson, M. Tepfer, Arch. Virol. 157, 483–495 (2012)

    Article  PubMed  CAS  Google Scholar 

  29. P.S. Wyant, D. Gotthardt, B. Schäfer, B. Krenz, H. Jeske, Arch. Virol. 156, 347–352 (2011)

    Article  PubMed  CAS  Google Scholar 

  30. R.W. Briddon, B.L. Patil, B. Bagewadi, M.S. Nawaz-ul-Rehman, C.M. Fauquet, BMC Evol. Biol. 10, 97 (2010)

    Article  PubMed  PubMed Central  Google Scholar 

  31. E. Regel, in Gartenflora, ed. by E. Regel (Ferdinand Enke, Stuttgart, 1875), pp. 116–117

    Google Scholar 

  32. C.W. Bennett, The Curly Top Disease of Sugarbeet and Other Plants (American Phytopathological Society, St. Paul, 1971)

    Google Scholar 

  33. K. Saunders, I.D. Bedford, T. Yahara, J. Stanley, Nature 422, 831 (2003)

    Article  PubMed  CAS  Google Scholar 

  34. S. Garcia-Andres, D.M. Tomas, S. Sanchez-Campos, J. Navas-Castillo, E. Moriones, Virology 365, 210–219 (2007)

    Article  PubMed  CAS  Google Scholar 

  35. S. Duffy, E.C. Holmes, Appl. Environ. Microbiol. 73, 7114–7117 (2007)

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  36. A.M. Idris, A. Abdel-Salam, J.K. Brown, Plant Dis. 90, 1262 (2006)

    Article  Google Scholar 

  37. M. Quinones, M.E. Fonseca, Y. Martinez, G.P. Accotto, Plant Dis. 86, 73 (2002)

    Article  Google Scholar 

  38. K. Saunders, I.D. Bedford, J. Stanley, J. Gen. Virol. 83, 907–913 (2002)

    PubMed  CAS  Google Scholar 

  39. E. Fiallo-Olivé, Y. Martínez-Zubiaur, E. Moriones, J. Navas-Castillo, Virology 426, 1–6 (2012)

    Article  PubMed  Google Scholar 

  40. K. Rosario, P. Padilla-Rodriguez, S. Kraberger, D. Stainton, D.P. Martin, M. Breitbart, A. Varsani, Virus Res. 171, 231–237 (2013)

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors like to thank Drs. Björn Krenz, Arvind Varsani and Christina Wege for critical reading of the manuscript. We are grateful to Kerstin Kläring (Technical Head of the Botanical Garden Berlin-Potsdam) for providing Peristrophe speciosa plants. This research was supported by the ERA-PG programme (RCA Genomics, BMBF 0313986).

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Authors and Affiliations

  1. Institute of Biology, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70550, Stuttgart, Germany

    Holger Jeske, Sigrid Kober, Benjamin Schäfer & Stephan Strohmeier

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  1. Holger Jeske
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  2. Sigrid Kober
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  3. Benjamin Schäfer
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  4. Stephan Strohmeier
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Correspondence to Holger Jeske.

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Jeske, H., Kober, S., Schäfer, B. et al. Circomics of Cuban geminiviruses reveals the first alpha-satellite DNA in the Caribbean. Virus Genes 49, 312–324 (2014). https://doi.org/10.1007/s11262-014-1090-8

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